immuneSIM {immuneSIM}

Simulates an immune repertoire based on user-defined parameters

Description

Simulates an immune repertoire based on user-defined parameters

Usage

immuneSIM(number_of_seqs = 1000,
  vdj_list = list_germline_genes_allele_01, species = "mm",
  receptor = "ig", chain = "h",
  insertions_and_deletion_lengths = insertions_and_deletion_lengths_df,
  user_defined_alpha = 2, name_repertoire = "sim_rep",
  length_distribution_rand = length_dist_simulation, random = FALSE,
  shm.mode = "none", shm.prob = 15/350, vdj_noise = 0,
  vdj_dropout = c(V = 0, D = 0, J = 0), ins_del_dropout = c(""),
  equal_cc = FALSE, freq_update_time = round(0.5 * number_of_seqs),
  max_cdr3_length = 100, min_cdr3_length = 6, verbose = TRUE,
  airr_compliant = TRUE)

Arguments

number_of_seqs

Integer defining the number of sequences that should be simulated

vdj_list

List containing germline genes and their frequencies

species

String defining species for which repertoire should be simulated ("mm": mouse, "hs": human. Default: "mm").

receptor

String defining receptor type ("ig" or "tr". Default: "ig")

chain

String defining chain (for ig: "h","k","l", for tr: "b" or "a". Default: "h")

insertions_and_deletion_lengths

Data.frame containing np1, np2 sequences as well as deletion lengths. (Pooled from murine repertoire data, Greiff,2017) Note: This is a subset of 500000 observations of the dataframe used in the paper. The full dataframe which can be introduced here can be found on: (Git-Link)

user_defined_alpha

Numeric. Scaling parameter used for the simulation of powerlaw distribution (recommended range 2-5. Default: 2, https://en.wikipedia.org/wiki/Power_law)

name_repertoire

String defining chosen repertoire name recorded in the name_repertoire column of the output for identification.

length_distribution_rand

Vector containing lengths of immune receptor sequences based on immune repertoire data (Greiff, 2017).

random

Boolean. If TRUE repertoire will consist of fully random sequences, independent of germline genes.

shm.mode

String defining mode of somatic hypermutation simulation based on AbSim (options: 'none', 'data','poisson', 'naive', 'motif', 'wrc'. Default: 'none'). See AbSim documentation.

shm.prob

Numeric defining probability of a SHM (somatic hypermutation) occurring at each position.

vdj_noise

Numeric between 0,1, setting noise level to be introduced in provided V,D,J germline frequencies. 0 denotes no noise. (Default: 0)

vdj_dropout

Named vector containing entries V,D,J setting the number of germline genes to be dropped out. (Default: c("V"=0,"D"=0,"J"=0))

ins_del_dropout

String determining whether insertions and deletions should occur. Options: "", "no_insertions", "no_insertions_n1", "no_insertions_n2", "no_deletions_v", "no_deletions_d_5", "no_deletions_d_3", "no_deletions_j", "no_deletions_vd", "no_deletions". Default: "")

equal_cc

Boolean that if set TRUE will override user_defined_alpha and generate a clone count distribution that is equal for all sequences. Default: FALSE.

freq_update_time

Numeric determining whether simulated VDJ frequencies agree with input after set amount of sequences to correct for VDJ bias. Default: Update after 50 percent of sequences.

max_cdr3_length

Numeric defining maximal length of cdr3. (Default: 100)

min_cdr3_length

Numeric defining minimal length of cdr3. (Default: 6)

verbose

Boolean toggling printing of progress on and off (Default: FALSE)

airr_compliant

Boolean determining whether output repertoire should be named in an AIRR compliant manner (Default: TRUE). (http://docs.airr-community.org/en/latest/)

Value

An annotated AIRR-compliant immuneSIM repertoire. (http://docs.airr-community.org/en/latest/)

Examples

sim_rep <- immuneSIM(number_of_seqs = 10, vdj_list = list_germline_genes_allele_01,
species = "mm", receptor = "ig", chain = "h",
insertions_and_deletion_lengths = insertions_and_deletion_lengths_df,
user_defined_alpha = 2,name_repertoire = "mm_igh_sim",
shm.mode = "data",shm.prob=15/350,vdj_noise = 0, vdj_dropout = c(V=0,D=0,J=0),
ins_del_dropout = "",min_cdr3_length = 6)